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Crystal structure of Mcl-1 in complex with an Mcl-1 selective BH3 ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NL9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.75 298 0.2M Zinc Acetate, 0.2M Imidazole, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.51 51.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.171 α = 90 b = 69.635 β = 90 c = 120.654 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ Capillary optics (AXCO) 2006-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.03 60.3 98.71 0.044 3.2 13365 5.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.03 2.1 96.1 0.204 3.1 3.1 1357
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2NL9 2.03 50 2 13365 710 98.71 0.19441 0.19201 0.1897 0.24108 0.2345 RANDOM 27.253
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.47 -0.51 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.358 r_dihedral_angle_4_deg 18.131 r_dihedral_angle_3_deg 15.074 r_dihedral_angle_1_deg 4.209 r_scangle_it 3.658 r_scbond_it 2.363 r_mcangle_it 1.624 r_angle_refined_deg 1.194 r_mcbond_it 0.967 r_symmetry_hbond_refined 0.362
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.358 r_dihedral_angle_4_deg 18.131 r_dihedral_angle_3_deg 15.074 r_dihedral_angle_1_deg 4.209 r_scangle_it 3.658 r_scbond_it 2.363 r_mcangle_it 1.624 r_angle_refined_deg 1.194 r_mcbond_it 0.967 r_symmetry_hbond_refined 0.362 r_nbtor_refined 0.296 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.198 r_metal_ion_refined 0.089 r_chiral_restr 0.086 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1357 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing